/* codeml_leo.h
*/

#ifndef CODEML_H
#define CODEML_H

#include <vector>
#include <string>
#include <iostream>
#include "codeml_results.h"

namespace BioCPP
{


enum eDNDS_PROGRAM {eCODEML, eYN00};
enum eCODEML_CODON {eF61, eF3x4};
void prepare_temp_directory(const std::string&				tmp_path,
							bool							fixed_kappa,
							float							kappa,
							eDNDS_PROGRAM					dnds_program,
							eCODEML_CODON					f61,
							bool&							directory_created);
bool kaks_analyse (			std::string		 				seq1,
							std::string 					seq2,
							unsigned						seq_tag1,
							unsigned						seq_tag2,
							std::vector<t_codeml_results>&	results,
							const std::string&				dnds_exe_path,
							eDNDS_PROGRAM					dnds_program,
							unsigned&						cnt_hung_paml_restarted);
};
#endif
